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Data Integration, Mass Spectrometry Proteomics Software Development

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Neil Swainston
Neil Swainston

This document discusses quantitative proteomics and integrating proteomics data into kinetic modeling in systems biology. It describes using isotopically labeled peptides to quantify proteins simultaneously via mass spectrometry. A method called QconCAT is outlined which uses an artificial protein containing multiple labeled peptides to reference. The document then describes an informatics pipeline to analyze such quantitative proteomics data, identifying peptides, determining concentrations, uploading data to repositories, and linking it with modeling databases to incorporate experimental data into systems biology simulations.

Technology
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Overview ,[object Object],[object Object]
A typical proteomics experiment ,[object Object],Separating by size or charge in most cases Identify peptides as a proxy for proteins, comparing theoretical to experimental spectra
Quantitative proteomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Quantitative proteomics ,[object Object],[object Object],[object Object],[object Object]
Quantitative proteomics
Quantitative proteomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Quantitative proteomics ,[object Object],[object Object],[object Object],[object Object]
Mixture 40:60 Data: Kathleen Carroll (Orbitrap MS) Quantitative proteomics: QconCAT
Quantitative proteomics: QconCAT ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Quantitative proteomics: QconCAT ,[object Object],[object Object],[object Object]
[object Object],Quantitative proteomics: QconCAT
… from instrument to browser ,[object Object],[object Object],[object Object],[object Object]
Selection of QconCAT peptides ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
QconCAT Selection Wizard ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 
QconCAT… Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Pratt JM, et al. Nature Protocols 1, 1029-1043 (2006)
QconCAT data analysis ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
Pride Converter ,[object Object],[object Object],[object Object],[object Object],[object Object]
Pride Converter
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
QconCAT PrideWizard: Identify ,[object Object],[object Object],[object Object],[object Object]
 
QconCAT PrideWizard: Identify ,[object Object]
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
QconCAT PrideWizard: Quantify ,[object Object],[object Object],[object Object]
QconCAT PrideWizard: Quantify ,[object Object],[object Object]
QconCAT PrideWizard: Quantify ,[object Object],[object Object]
QconCAT PrideWizard: Quantify ,[object Object]
QconCAT PrideWizard: Quantify ,[object Object]
QconCAT PrideWizard: Quantify ,[object Object]
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
QconCAT data analysis eXist database PRIDE XML Identify QconCAT Pride Wizard Quantify Format Upload Web / web service Browser Mascot PRIDE XML PRIDE Converter mzData
MCISB Proteome Database ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
QconCAT informatics pipeline ,[object Object],[object Object]
Data Integration
Systems biology modelling Enzyme kinetics Quantitative metabolomics Quantitative proteomics Systems Biology Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE XML MeMo SABIO-RK Web service Web service Web service MeMo-RK Web service
Systems biology modelling Enzyme kinetics Quantitative metabolomics Quantitative proteomics Systems Biology Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE XML MeMo SABIO-RK Web service Web service Web service MeMo-RK Web service
Systems biology modelling Enzyme kinetics Quantitative metabolomics Quantitative proteomics Systems Biology Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE XML MeMo SABIO-RK Web service Web service Web service MeMo-RK Web service
Systems biology modelling Enzyme kinetics Quantitative metabolomics Quantitative proteomics Systems Biology Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE XML MeMo SABIO-RK Web service Web service Web service MeMo-RK Web service
Modelling life-cycle workflows
From experiment to simulation Kinetic models Experimental data Systematic integration of experimental data and models in systems biology. Li P, et al. BMC Bioinformatics . 2010, 11 :582.
Conclusion ,[object Object],[object Object],[object Object],[object Object],[object Object]
Thanks…
 

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